Split paired FASTQ files into smaller files with a target number of reads each.

Requirements

• a C++ compiler with C++11 support

Download and installation

Either clone the repository:

$ git clone https://github.com/fnadalin/fastqsplit.git

or download and decompress the tarball archive:

$ wget https://github.com/fnadalin/fastqsplit/-/archive/master/fastqsplit-master.tar.gz
$ tar -xzf fastqsplit-master.tar.gz fastqsplit

To compile the code:

$ cd fastqsplit
$ make

The installation takes < 1 second on a desktop computer. The software has been tested on version v1.0.0.

Instructions

To run fastqsplit:

$ ./fastqsplit <R1.fastq> <R2.fastq> <nseq> <outdir>

where nseq is the target number of reads per file.